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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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-<head>
-<title>Building Jalview from Source</title>
-</head>
-<body>
-<h1>Building Jalview from Source</h1>
-<P>
-<p>
-You will need the following (hopefully):<br>
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+</head><body>
+<h1 id="building-jalview-from-source">Building Jalview from Source</h1>
+<h2 id="what-you-will-need">What you will need</h2>
+<p>The method here is described in terms of using a command line. You can easily do this on linux or in a Terminal window in macOS. You can do it in Windows.</p>
<ul>
-<li>Java development kit (JDK1.6 is the recommended platform for developing with Jalview, although JDK1.7 seems to work too!).</li>
-<li>Ant (we think 1.5.4 is quite sufficient to use the simple build
-file supplied, and it seems to work with later versions e.g. 1.7).</li>
+<li>Java 11 compliant JDK</li>
+<li>gradle 5.1 or above</li>
+<li>git</li>
</ul>
-With any luck, after setting your paths and JAVA_HOME correctly, you
-just need to change to the Jalview directory and run ant (this works
-from JBuilder and eclipse too, but NetBeans is a bit trickier).
-<pre>
- ant
-</pre>
+<h3 id="java-11-jdk">Java 11 JDK</h3>
+<p>We recommend obtaining an OpenJDK JDK 11 from AdoptOpenJDK: <a href="https://adoptopenjdk.net/?variant=openjdk11&jvmVariant=hotspot" class="uri">https://adoptopenjdk.net/?variant=openjdk11&jvmVariant=hotspot</a>, either the <em>Installer</em> or <code>.zip</code>/<code>.tar.gz</code> variants whichever you prefer (if you’re not sure, choose the <em>Installer</em>).</p>
+<h3 id="gradle-and-git"><code>gradle</code> and <code>git</code></h3>
+<p>You should be able to install the latest (or close to the latest) versions of gradle and git using your OS package manager.</p>
+<p>For <strong>macOS</strong> we recommend using <code>brew</code>, which can be installed following the instructions at <a href="https://brew.sh/" class="uri">https://brew.sh/</a>. After installing <code>brew</code>, open a Terminal window and type in (using an Administrator privileged user): <code>brew install gradle git</code> or <code>brew upgrade gradle git</code> if you already have them installed but need to upgrade the version.</p>
+<p>For <strong>linux</strong> this will depend on which distribution you’re using. For <em>debian</em> based distributions (e.g. Mint, Ubuntu, Debian) run <code>sudo apt-get install gradle git</code> whilst for RPM-based distributions run (probably) <code>sudo yum install gradle git</code> If you have some other version of linux you’ll probably be able to work it out!</p>
+<p>For <em>Windows</em> users, you might do well by using the <strong>Chocolatey</strong> package manager. See install instructions at <a href="https://chocolatey.org/" class="uri">https://chocolatey.org/</a>, and you will just need <code>choco install gradle git</code> Alternatively, you could install a real <code>bash</code> shell and install both <code>gradle</code> and <code>git</code> through <code>apt-get</code>. Another alternative would be to install them separately following the instructions at <a href="https://gradle.org/install/" class="uri">https://gradle.org/install/</a>, and for <code>git</code> here are a couple of suggestions: Git for Windows <a href="https://gitforwindows.org/" class="uri">https://gitforwindows.org/</a> or a real <code>bash</code>-shell <a href="https://devblogs.microsoft.com/commandline/bash-on-ubuntu-on-windows-download-now-3/" class="uri">https://devblogs.microsoft.com/commandline/bash-on-ubuntu-on-windows-download-now-3/</a> !</p>
+<h2 id="section"></h2>
-</p>
-<p><strong>Building a webstart version of jalview</strong></p>
-Jalview depends on several libraries contained in the libs directory
-of the distribution. In order to access them, they must all be signed
-jars - using the same jarsigner key as jalview itself. There is a
-build target in ant to make the signed jar files in a directory called
-dist. But first you need to make your own key:
-<p><strong>Making your own key</strong></p>
-
- <p>The ant 'makefulldist' target assumes that a keystore exists in
- a directory 'keys'. To make a key accessible using the default
- settings in the build.xml file then make the keys directory and add
- the jarsigner key with the following :</p>
- <pre>mkdir keys</pre>
- <pre>keytool -genkey -keystore keys/.keystore -keypass alignmentisfun
- -storepass alignmentisfun -sigalg SHA1withRSA -keyalg RSA -alias jalview</pre>
- <em>(you will have to answer some personal questions here)</em>
- <pre>ant makedist -DWebStartLocation="file://.pathtojalviewsource./dist" -Dapplication.codebase="*"</pre>
- <p>This should eventually generate a jalview.jnlp file in ./dist
- along with a set of signed jars using the jalview key). In order to
- test locally via webstart you'll now need to add 'file:/' to your
- java webstart security exception list. Then:</p>
- <pre>javaws file://.pathtojalviewsource./dist/jalview.jnlp</pre>
- <p>Please remember to remove that entry afterwards, since it will leave
- your system vulnerable to malicious code.
- </p>
- <p>
- <strong>Building the JalviewLite applet<br>
- </strong> The JalviewLite applet is compiled using a subset of the packages in
- the src directory (specifically: MCView, and jalview.{datamodel,
- analysis, appletgui, utils, schemes, api, structure}, and
- com.stevesoft.*). Once compiled, these class files are obfuscated to
- make the code run efficiently. To compile the applet Jar, use the
- makeApplet task - optionally passing in a 'donotobfuscate' property to
- the ant build (e.g. -Ddonotobfuscate=true) to disable obfuscation. </p><p>
- The ant target 'pubapplet' can be used to compile install the
- jalviewApplet.jar and any dependent jars (under appletlib) into a copy
- of the examples directory created under the <em>outputDir</em> build
- property (which defaults to the 'dist' directory).
- </p>
- <p>
-<h1>using IDEs to build Jalview</h1>
- <p>The Jalview source distribution includes project definitions for
- Eclipse, Netbeans and some rather ancient Borland JBuilder .jpx
- project files. These files should be sufficient to set up basic source
- folders and build paths, but you will need to ensure that all .jar
- files in the lib and appletlib directories are added to the build path
- for your IDE project, and that the 'buildindices' target in Jalview's
- build.xml is executed with the 'outputDir' ant property set to the
- directory where the IDE expects to place compiled classes ('classes'
- directory for eclipse, 'build/classes' for netbeans).</p>
- <p>Note: It is generally not recommended that you distribute build
- artefacts that were generated automatically via an IDE's own packaging
- mechanism (e.g. Netbeans' executable Jar and dependent lib directory).
- The hand-crafted ant build.xml is (currently) the only officially
- supported method of building distributable versions of Jalview.</p>
-<address>
-<a href="mailto:help@jalview.org">Jalview development team</a>
-</address>
-</body>
-</html>
+</body></html>
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